TOLB - ECOLI - GREMLIN Contacts

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TOLB - Protein TolB

UniProt:	P0A855	Sequences: MKQALRVAFGFLILWASVLHAEVRIVIDSGVDSGRPIGVVPFQWAGPGAAPEDIGGIVAADLRNSGKFNPLDRARLPQQPGSAQEVQPAAWSALGIDAVVVGQVTPNPDGSYNVAYQLVDTGGAPGTVLAQNSYKVNKQWLRYAGHTASDEVFEKLTGIKGAFRTRIAYVVQTNGGQFPYELRVSDYDGYNQFVVHRSPQPLMSPAWSPDGSKLAYVTFESGRSALVIQTLANGAVRQVASFPRHNGAPAFSPDGSKLAFALSKTGSLNLYVMDLASGQIRQVTDGRSNNTEPTWFPDSQNLAFTSDQAGRPQVYKVNINGGAPQRITWEGSQNQDADVSSDGKFMVMVSSNGGQQHIAKQDLATGGVQVLSSTFLDETPSLAPNGTMVIYSSSQGMGSVLNLVSTDGRFKARLPATDGQVKFPAWSPYL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11008
Length:	430 (358)
Sequences:	586 (489)
Seq/√Len:	25.9

ECOLI - TOLB
BACSU - YWHL

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
242_F	260_F	4.469	1.00
297_P	343_G	3.872	1.00
96_I	103_Q	3.737	1.00
215_A	258_L	3.592	1.00
216_Y	229_Q	3.449	1.00
198_S	229_Q	3.279	1.00
348_M	361_Q	3.201	1.00
242_F	246_N	3.197	1.00
347_V	382_L	3.142	1.00
270_L	304_F	3.082	1.00
184_V	187_Y	2.809	1.00
198_S	216_Y	2.746	0.99
259_A	262_L	2.662	0.99
304_F	315_Y	2.636	0.99
286_G	309_A	2.520	0.99
53_D	84_Q	2.495	0.99
257_K	260_F	2.317	0.98
207_W	295_W	2.303	0.98
215_A	251_F	2.264	0.98
349_V	377_D	2.195	0.97
34_G	40_V	2.152	0.97
94_L	104_V	2.111	0.97
313_Q	326_R	2.069	0.96
236_V	240_A	2.041	0.96
390_I	395_Q	2.016	0.96
182_L	187_Y	1.991	0.95
257_K	261_A	1.988	0.95
218_T	223_R	1.944	0.95
110_G	120_D	1.941	0.95
83_A	87_Q	1.919	0.94
293_P	304_F	1.909	0.94
58_V	66_G	1.897	0.94
76_L	79_Q	1.872	0.93
228_I	251_F	1.864	0.93
242_F	269_N	1.863	0.93
182_L	188_D	1.853	0.93
348_M	359_A	1.848	0.93
61_D	64_N	1.834	0.93
96_I	99_V	1.824	0.92
259_A	302_L	1.819	0.92
351_S	358_I	1.808	0.92
218_T	225_A	1.786	0.92
172_Q	175_G	1.781	0.92
385_N	391_Y	1.761	0.91
54_I	68_F	1.760	0.91
294_T	303_A	1.759	0.91
55_G	60_A	1.738	0.90
292_E	305_T	1.730	0.90
257_K	262_L	1.728	0.90
77_P	80_P	1.726	0.90
208_S	248_A	1.715	0.90
239_V	273_M	1.710	0.90
330_E	348_M	1.677	0.89
26_V	33_S	1.663	0.88
86_V	100_V	1.652	0.88
25_I	28_D	1.630	0.87
223_R	229_Q	1.630	0.87
154_E	160_K	1.616	0.87
38_G	42_F	1.615	0.87
95_G	99_V	1.614	0.87
273_M	315_Y	1.603	0.86
103_Q	107_N	1.600	0.86
191_N	310_G	1.599	0.86
23_V	27_I	1.598	0.86
158_G	161_G	1.597	0.86
95_G	98_A	1.589	0.86
248_A	261_A	1.583	0.86
136_V	156_L	1.561	0.85
267_S	286_G	1.558	0.85
296_F	340_S	1.524	0.84
285_D	315_Y	1.512	0.83
202_L	292_E	1.507	0.83
103_Q	109_D	1.503	0.83
259_A	263_S	1.495	0.82
182_L	186_D	1.495	0.82
100_V	107_N	1.491	0.82
25_I	30_G	1.483	0.82
51_P	55_G	1.460	0.81
127_T	139_Q	1.450	0.80
267_S	271_Y	1.445	0.80
262_L	269_N	1.435	0.80
261_A	293_P	1.429	0.79
181_E	185_S	1.425	0.79
225_A	251_F	1.422	0.79
61_D	72_D	1.421	0.79
238_Q	243_P	1.414	0.79
167_I	170_V	1.414	0.79
77_P	81_G	1.409	0.78
115_A	120_D	1.409	0.78
61_D	70_P	1.402	0.78
79_Q	113_N	1.399	0.78
28_D	32_D	1.397	0.78
112_Y	116_Y	1.386	0.77
183_R	187_Y	1.384	0.77
303_A	339_V	1.380	0.77
35_R	42_F	1.378	0.77
198_S	223_R	1.372	0.76
211_G	271_Y	1.372	0.76
85_E	90_A	1.364	0.76
128_V	131_Q	1.360	0.76
50_A	75_R	1.353	0.75
283_V	303_A	1.329	0.74
61_D	66_G	1.324	0.74
76_L	81_G	1.321	0.74
34_G	38_G	1.315	0.73
369_Q	372_S	1.308	0.73
90_A	95_G	1.302	0.72
261_A	309_A	1.301	0.72
254_D	342_D	1.299	0.72
150_D	163_F	1.294	0.72
316_K	364_A	1.291	0.72
91_W	102_G	1.285	0.71
58_V	61_D	1.283	0.71
226_L	260_F	1.282	0.71
90_A	100_V	1.272	0.71
146_H	149_S	1.271	0.71
223_R	260_F	1.266	0.70
75_R	78_Q	1.239	0.69
106_P	118_L	1.236	0.68
40_V	43_Q	1.234	0.68
137_N	140_W	1.231	0.68
62_L	65_S	1.229	0.68
306_S	326_R	1.223	0.68
54_I	58_V	1.220	0.67
138_K	272_V	1.213	0.67
79_Q	83_A	1.206	0.66
85_E	106_P	1.204	0.66
335_Q	350_S	1.203	0.66
381_S	388_M	1.200	0.66
30_G	36_P	1.195	0.66
270_L	293_P	1.195	0.66
202_L	205_P	1.194	0.66
97_D	104_V	1.194	0.66
255_G	306_S	1.190	0.65
121_T	166_R	1.185	0.65
98_A	105_T	1.176	0.64
305_T	348_M	1.175	0.64
103_Q	106_P	1.175	0.64
27_I	30_G	1.174	0.64
71_L	75_R	1.170	0.64
39_V	226_L	1.168	0.64
51_P	65_S	1.168	0.64
382_L	392_S	1.160	0.63
259_A	295_W	1.157	0.63
97_D	100_V	1.151	0.63
374_T	382_L	1.149	0.63
240_A	246_N	1.148	0.63
177_Q	180_Y	1.148	0.63
78_Q	81_G	1.147	0.62
136_V	143_Y	1.145	0.62
126_G	129_L	1.144	0.62
56_G	59_A	1.143	0.62
380_P	391_Y	1.142	0.62
66_G	69_N	1.141	0.62
146_H	161_G	1.138	0.62
261_A	290_N	1.129	0.61
251_F	275_L	1.128	0.61
339_V	346_M	1.126	0.61
360_K	383_A	1.125	0.61
334_N	350_S	1.117	0.60
226_L	249_P	1.109	0.60
134_Y	141_L	1.096	0.59
72_D	75_R	1.096	0.59
142_R	145_G	1.095	0.59
216_Y	307_D	1.088	0.58
390_I	393_S	1.086	0.58
97_D	105_T	1.079	0.58
343_G	346_M	1.075	0.57
312_P	337_A	1.074	0.57
93_A	97_D	1.070	0.57
99_V	104_V	1.069	0.57
386_G	389_V	1.068	0.57
114_V	117_Q	1.051	0.56
164_R	167_I	1.050	0.56
144_A	155_K	1.039	0.55
215_A	259_A	1.036	0.55
305_T	334_N	1.032	0.54
96_I	100_V	1.027	0.54
246_N	260_F	1.024	0.54
184_V	190_Y	1.023	0.54
129_L	137_N	1.021	0.53
186_D	189_G	1.020	0.53
242_F	271_Y	1.012	0.53
116_Y	120_D	1.009	0.53
285_D	311_R	1.002	0.52
141_L	152_V	0.996	0.52
28_D	38_G	0.994	0.51
71_L	80_P	0.993	0.51
258_L	261_A	0.993	0.51
55_G	62_L	0.984	0.51
179_P	183_R	0.983	0.51
65_S	68_F	0.976	0.50
370_V	373_S	0.975	0.50
111_S	114_V	0.975	0.50
92_S	103_Q	0.973	0.50
158_G	163_F	0.972	0.50
63_R	117_Q	0.971	0.50
99_V	121_T	0.969	0.50
94_L	102_G	0.968	0.50
129_L	239_V	0.966	0.49
270_L	302_L	0.964	0.49
33_S	36_P	0.963	0.49
231_L	291_T	0.957	0.49
327_I	375_F	0.954	0.49
304_F	309_A	0.953	0.48
310_G	335_Q	0.953	0.48
337_A	347_V	0.948	0.48
205_P	216_Y	0.947	0.48
104_V	108_P	0.945	0.48
178_F	182_L	0.944	0.48
60_A	64_N	0.942	0.48
297_P	341_S	0.941	0.48
140_W	144_A	0.941	0.48
195_V	303_A	0.939	0.47
142_R	158_G	0.939	0.47
60_A	63_R	0.934	0.47
113_N	121_T	0.928	0.47
294_T	382_L	0.927	0.47
380_P	390_I	0.925	0.46
224_S	229_Q	0.924	0.46
58_V	65_S	0.923	0.46
350_S	359_A	0.923	0.46
377_D	380_P	0.922	0.46
102_G	158_G	0.921	0.46
274_D	277_S	0.918	0.46
212_S	230_T	0.918	0.46
134_Y	137_N	0.915	0.46
148_A	153_F	0.914	0.46
138_K	142_R	0.913	0.46
23_V	30_G	0.910	0.45
259_A	293_P	0.910	0.45
56_G	60_A	0.910	0.45
237_R	240_A	0.907	0.45
290_N	295_W	0.905	0.45
360_K	364_A	0.903	0.45
104_V	107_N	0.902	0.45
205_P	255_G	0.900	0.45
203_M	247_G	0.898	0.44
249_P	255_G	0.898	0.44
101_V	106_P	0.896	0.44
104_V	115_A	0.887	0.44
238_Q	241_S	0.887	0.44
145_G	149_S	0.886	0.44
165_T	170_V	0.884	0.43
227_V	248_A	0.883	0.43
32_D	47_P	0.882	0.43
346_M	361_Q	0.880	0.43
60_A	74_A	0.880	0.43
99_V	107_N	0.878	0.43
24_R	28_D	0.877	0.43
330_E	361_Q	0.875	0.43
142_R	188_D	0.874	0.43
332_S	349_V	0.868	0.42
64_N	72_D	0.863	0.42
104_V	110_G	0.860	0.42
146_H	182_L	0.860	0.42
286_G	306_S	0.859	0.42
154_E	157_T	0.858	0.42
253_P	299_S	0.854	0.41
215_A	295_W	0.854	0.41
197_R	218_T	0.851	0.41
61_D	65_S	0.851	0.41
383_A	393_S	0.849	0.41
34_G	41_P	0.849	0.41
180_Y	183_R	0.848	0.41
90_A	96_I	0.847	0.41
272_V	295_W	0.846	0.41
257_K	263_S	0.842	0.40
139_Q	179_P	0.840	0.40
59_A	67_K	0.836	0.40
215_A	228_I	0.833	0.40
90_A	102_G	0.833	0.40
133_S	141_L	0.832	0.40
95_G	101_V	0.832	0.40
142_R	163_F	0.832	0.40
249_P	315_Y	0.827	0.39
280_I	283_V	0.825	0.39
168_A	171_V	0.819	0.39
336_D	387_T	0.815	0.38
60_A	80_P	0.812	0.38
33_S	43_Q	0.809	0.38
23_V	31_V	0.809	0.38
51_P	54_I	0.808	0.38
62_L	66_G	0.805	0.38
166_R	170_V	0.803	0.38
95_G	104_V	0.800	0.37
94_L	97_D	0.799	0.37
306_S	313_Q	0.798	0.37
134_Y	140_W	0.797	0.37
211_G	278_G	0.796	0.37
146_H	156_L	0.791	0.37
334_N	337_A	0.791	0.37
267_S	273_M	0.790	0.37
130_A	133_S	0.788	0.37
83_A	93_A	0.784	0.36
260_F	263_S	0.784	0.36
46_G	49_A	0.782	0.36
290_N	334_N	0.780	0.36
120_D	170_V	0.779	0.36
146_H	152_V	0.778	0.36
211_G	286_G	0.777	0.36
180_Y	184_V	0.776	0.36
149_S	186_D	0.772	0.36
113_N	116_Y	0.770	0.35
109_D	112_Y	0.765	0.35
231_L	306_S	0.763	0.35
260_F	281_R	0.759	0.35
85_E	93_A	0.758	0.35
89_A	105_T	0.757	0.35
106_P	115_A	0.755	0.34
105_T	111_S	0.754	0.34
29_S	39_V	0.752	0.34
230_T	235_A	0.750	0.34
35_R	43_Q	0.749	0.34
101_V	111_S	0.749	0.34
120_D	158_G	0.748	0.34
391_Y	395_Q	0.747	0.34
57_I	65_S	0.746	0.34
85_E	88_P	0.746	0.34
204_S	207_W	0.745	0.34
94_L	100_V	0.744	0.34
349_V	380_P	0.744	0.34
76_L	80_P	0.742	0.34
216_Y	224_S	0.739	0.33
59_A	66_G	0.739	0.33
158_G	170_V	0.739	0.33
228_I	292_E	0.738	0.33
97_D	111_S	0.737	0.33
49_A	81_G	0.736	0.33
104_V	112_Y	0.733	0.33
379_T	390_I	0.732	0.33
348_M	352_N	0.732	0.33
128_V	133_S	0.731	0.33
25_I	39_V	0.728	0.33
388_M	395_Q	0.725	0.32
270_L	280_I	0.724	0.32
24_R	35_R	0.723	0.32
79_Q	127_T	0.723	0.32
45_A	48_G	0.717	0.32
146_H	153_F	0.715	0.32
293_P	303_A	0.715	0.32
57_I	61_D	0.713	0.32
55_G	63_R	0.713	0.32
346_M	367_G	0.713	0.32
214_L	248_A	0.712	0.32
202_L	218_T	0.710	0.31
369_Q	376_L	0.707	0.31
131_Q	166_R	0.702	0.31
381_S	390_I	0.700	0.31
110_G	113_N	0.698	0.31
56_G	63_R	0.694	0.30
53_D	59_A	0.691	0.30
181_E	187_Y	0.688	0.30
29_S	50_A	0.684	0.30
102_G	106_P	0.682	0.30
173_T	176_G	0.680	0.30
92_S	100_V	0.679	0.30
29_S	33_S	0.678	0.29
115_A	119_V	0.677	0.29
346_M	358_I	0.677	0.29
153_F	161_G	0.677	0.29
142_R	149_S	0.674	0.29
224_S	315_Y	0.674	0.29
377_D	393_S	0.674	0.29
58_V	77_P	0.667	0.29
363_L	367_G	0.665	0.29
88_P	93_A	0.664	0.29
275_L	283_V	0.664	0.29
224_S	235_A	0.662	0.28
62_L	70_P	0.662	0.28
43_Q	62_L	0.660	0.28
205_P	336_D	0.658	0.28
93_A	96_I	0.657	0.28
184_V	188_D	0.657	0.28
365_T	368_V	0.655	0.28
121_T	130_A	0.654	0.28
242_F	262_L	0.652	0.28
27_I	35_R	0.652	0.28
152_V	186_D	0.651	0.28
380_P	386_G	0.650	0.28
306_S	311_R	0.650	0.28
216_Y	248_A	0.650	0.28
375_F	379_T	0.647	0.28
316_K	362_D	0.646	0.28
252_S	255_G	0.644	0.27
49_A	106_P	0.643	0.27
263_S	358_I	0.641	0.27
180_Y	187_Y	0.640	0.27
114_V	118_L	0.639	0.27
103_Q	125_P	0.636	0.27
303_A	350_S	0.634	0.27
170_V	190_Y	0.631	0.27
149_S	152_V	0.630	0.27
387_T	394_S	0.628	0.26
290_N	305_T	0.625	0.26
218_T	299_S	0.625	0.26
98_A	117_Q	0.622	0.26
205_P	249_P	0.620	0.26
276_A	379_T	0.616	0.26
298_D	343_G	0.616	0.26
73_R	79_Q	0.616	0.26
143_Y	155_K	0.616	0.26
346_M	363_L	0.613	0.26
95_G	181_E	0.606	0.25
249_P	344_K	0.606	0.25
262_L	267_S	0.605	0.25
365_T	393_S	0.603	0.25
23_V	33_S	0.601	0.25
148_A	154_E	0.600	0.25
72_D	80_P	0.596	0.25
239_V	325_Q	0.596	0.25
90_A	103_Q	0.596	0.25
23_V	28_D	0.595	0.25
47_P	75_R	0.595	0.25
60_A	69_N	0.594	0.25
242_F	267_S	0.593	0.25
117_Q	131_Q	0.591	0.24
377_D	395_Q	0.588	0.24
32_D	35_R	0.588	0.24
92_S	105_T	0.586	0.24
208_S	245_H	0.584	0.24
57_I	62_L	0.583	0.24
91_W	106_P	0.580	0.24
89_A	103_Q	0.580	0.24
89_A	96_I	0.580	0.24
151_E	183_R	0.580	0.24
203_M	224_S	0.580	0.24
146_H	154_E	0.577	0.24
74_A	80_P	0.577	0.24
163_F	169_Y	0.576	0.24
315_Y	359_A	0.576	0.24
105_T	108_P	0.576	0.24
96_I	116_Y	0.575	0.24
382_L	386_G	0.574	0.24
249_P	269_N	0.573	0.23
246_N	302_L	0.572	0.23
24_R	29_S	0.571	0.23
133_S	137_N	0.571	0.23
310_G	326_R	0.571	0.23
218_T	247_G	0.571	0.23
254_D	343_G	0.570	0.23
248_A	290_N	0.569	0.23
130_A	144_A	0.568	0.23
65_S	69_N	0.568	0.23
290_N	293_P	0.568	0.23
171_V	180_Y	0.566	0.23
148_A	163_F	0.566	0.23
103_Q	115_A	0.565	0.23
103_Q	126_G	0.565	0.23
54_I	61_D	0.563	0.23
294_T	348_M	0.562	0.23
55_G	75_R	0.561	0.23
30_G	33_S	0.561	0.23
133_S	140_W	0.560	0.23
375_F	394_S	0.558	0.23
28_D	31_V	0.558	0.23
390_I	394_S	0.557	0.23
45_A	89_A	0.555	0.23
311_R	346_M	0.553	0.22
364_A	367_G	0.553	0.22
379_T	389_V	0.551	0.22
60_A	72_D	0.549	0.22
56_G	69_N	0.547	0.22
62_L	67_K	0.547	0.22
171_V	179_P	0.546	0.22
172_Q	180_Y	0.545	0.22
289_N	305_T	0.545	0.22
27_I	43_Q	0.544	0.22
132_N	144_A	0.543	0.22
281_R	316_K	0.542	0.22
101_V	115_A	0.541	0.22
89_A	104_V	0.540	0.22
55_G	72_D	0.540	0.22
330_E	350_S	0.539	0.22
56_G	71_L	0.539	0.22
285_D	309_A	0.538	0.22
211_G	251_F	0.537	0.22
144_A	152_V	0.536	0.22
232_A	237_R	0.536	0.22
74_A	81_G	0.535	0.22
166_R	172_Q	0.535	0.22
203_M	348_M	0.535	0.22
202_L	216_Y	0.533	0.21
168_A	174_N	0.533	0.21
149_S	153_F	0.533	0.21
91_W	186_D	0.532	0.21
164_R	168_A	0.532	0.21
109_D	116_Y	0.531	0.21
335_Q	348_M	0.530	0.21
117_Q	159_I	0.530	0.21
133_S	144_A	0.530	0.21
300_Q	318_N	0.528	0.21
349_V	359_A	0.528	0.21
85_E	108_P	0.528	0.21
142_R	186_D	0.528	0.21
193_F	270_L	0.527	0.21
33_S	40_V	0.524	0.21
235_A	352_N	0.524	0.21
367_G	372_S	0.523	0.21
135_K	160_K	0.523	0.21
132_N	138_K	0.522	0.21
98_A	108_P	0.522	0.21
33_S	85_E	0.520	0.21
198_S	227_V	0.520	0.21
114_V	120_D	0.520	0.21
91_W	94_L	0.520	0.21
99_V	152_V	0.519	0.21
104_V	118_L	0.519	0.21
125_P	129_L	0.518	0.21
182_L	189_G	0.518	0.21
27_I	37_I	0.518	0.21
210_D	226_L	0.518	0.21
94_L	106_P	0.517	0.21
257_K	274_D	0.516	0.21
217_V	352_N	0.516	0.21
81_G	103_Q	0.515	0.21
165_T	168_A	0.515	0.21
315_Y	348_M	0.514	0.20
58_V	71_L	0.514	0.20
377_D	391_Y	0.513	0.20
202_L	362_D	0.513	0.20
27_I	36_P	0.513	0.20
132_N	155_K	0.512	0.20
67_K	83_A	0.512	0.20
342_D	363_L	0.511	0.20
55_G	59_A	0.510	0.20
64_N	74_A	0.510	0.20
136_V	166_R	0.509	0.20
306_S	309_A	0.509	0.20
23_V	40_V	0.507	0.20
156_L	163_F	0.506	0.20
89_A	100_V	0.505	0.20
113_N	117_Q	0.505	0.20
102_G	116_Y	0.503	0.20
142_R	169_Y	0.502	0.20
349_V	353_G	0.501	0.20
52_E	114_V	0.500	0.20

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
2hqsA	2	0.9419	100	0.477	Contact Map
1vyhC	1	0.5442	100	0.513	Contact Map
4u1eI	1	0.5302	100	0.516	Contact Map
2ymuA	1	0.5395	100	0.517	Contact Map
5a1uC	1	0.5256	100	0.524	Contact Map
4j87A	1	0.5302	100	0.526	Contact Map
3fm0A	1	0.5302	100	0.526	Contact Map
3j80g	1	0.5349	100	0.527	Contact Map
4j73A	1	0.5349	100	0.527	Contact Map
4bpeR	1	0.5419	100	0.527	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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